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<p>Hi Vincent,</p>
<p><br>
</p>
<p>Could you maybe send the charm_report.html file to:
<a class="moz-txt-link-abbreviated" href="mailto:support@simnibs.org">support@simnibs.org</a></p>
<p><br>
</p>
<p>Happy to look at the data as well if you're allowed to share it.</p>
<p><br>
</p>
<p>Best,</p>
<p>Oula</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/5/22 12:11, Vincent Rochas wrote:<br>
</div>
<blockquote type="cite"
cite="mid:AM5PR0402MB2755FCC63CC47F1AA9D44A7198189@AM5PR0402MB2755.eurprd04.prod.outlook.com">
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<p class="MsoNormal ContentPasted0" style="margin:0cm 0cm
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Dear simNIBS users and programmers<o:p
class="ContentPasted0"> </o:p></p>
<p class="MsoNormal" style="margin:0cm 0cm
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<o:p class="ContentPasted0"> </o:p></p>
<p class="MsoNormal" style="margin:0cm 0cm
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I have used simNIBS previous versions with very good results
and reasonable simulations for tCS. I was using
<i class="ContentPasted0" style="color: inherit;
font-family: inherit; font-size: inherit;
font-variant-ligatures: inherit; font-variant-caps:
inherit; font-weight: inherit;">
headreco</i> function with two MRIs T1 and T2, converted
from Dicom to Nifti using SPM12.
<o:p class="ContentPasted0" style="color: inherit;
font-family: inherit; font-size: inherit; font-style:
inherit; font-variant-ligatures: inherit;
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</o:p></p>
<p class="MsoNormal" style="margin:0cm 0cm
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<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">I am now trying the new version of simNIBS
(4.0) using the
<i class="ContentPasted0">charm</i> function and
experiencing some troubles. <br class="ContentPasted0">
- The MRIs I was previously using are apparently not
compliant with the needed standard in term of orientation
(?) and there was a complain about sform and qform
annotation, so I was advised to use –forceqform by the
<i class="ContentPasted0">charm</i> function which I did.<o:p
class="ContentPasted0"> </o:p></span></p>
<p class="MsoNormal" style="margin:0cm 0cm
8pt;font-size:11pt;font-family:Calibri, sans-serif">
<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">- After using the –forceqform option it runs
the segmentation. However the resulting .msh file in the
m2m folder corresponds to another face and head than my
patient MRI!<o:p class="ContentPasted0"> </o:p></span></p>
<p class="MsoNormal" style="margin:0cm 0cm
8pt;font-size:11pt;font-family:Calibri, sans-serif">
<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">I tried to re-run the ernie segmentation
(without needing the –forceqform option). The command line
was like: charm ernie ernie_T1.nii.gz ernie_T2.nii.gz The
results is again this same face wrapped on ernie’s shape I
guess. Or Ernie’s head wrapped differently I don’t know.
<span style="mso-spacerun:yes" class="ContentPasted0"> </span>In
the case of the patient it is surely not the head and face
of the patient at all, and this same head though. Also the
segmentation of the cortex doesn’t look very precise,
sulci are not well delineated.
<o:p class="ContentPasted0"> </o:p></span></p>
<p class="MsoNormal" style="margin:0cm 0cm
8pt;font-size:11pt;font-family:Calibri, sans-serif">
<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">I then checked the log.html and I noticed a
difference with the examples provided by simNIBS (the
prototypic ernie segmentation). On the DEBUG line I have
'init_type': 'atlas' instead of 'init_type': mni' in the
example segmentation. <o:p class="ContentPasted0"> </o:p></span></p>
<p class="MsoNormal" style="margin:0cm 0cm
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<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">I don’t know if it is the problem but might
explain why it is differently sticking the atlas maybe on
the patient’s T1 as a result.
<o:p class="ContentPasted0"> </o:p></span></p>
<p class="MsoNormal" style="margin:0cm 0cm
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<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">That might be a trivial problem or an option
that I missed. I would be happy to have your opinion.<o:p
class="ContentPasted0"> </o:p></span></p>
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8pt;font-size:11pt;font-family:Calibri, sans-serif">
<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US"><br>
</span></p>
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<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">Best,<o:p class="ContentPasted0"> </o:p></span></p>
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<span style="mso-ansi-language:EN-US" class="ContentPasted0"
lang="EN-US">Vincent<o:p class="ContentPasted0"> </o:p></span></p>
<br>
</span></div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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